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Metagenomic binning suite

Project description

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GroopM is a metagenomic binning toolset. It leverages spatio-temoral
dynamics (differential coverage) to accurately (and almost automatically)
extract population genomes from multi-sample metagenomic datasets.

GroopM is largely parameter-free. Use: groopm -h for more info.

For installation and usage instructions see :

Data preparation and running GroopM

Before running GroopM you need to prep your data. A typical workflow looks like this:

1. Produce NGS data for your environment across mutiple (3+) samples (spearated spatially or temporally or both).
2. Co-assemble your reads using Velvet or similar.
3. For each sample, map the reads against the co-assembly. GroopM needs sorted indexed bam files. If you have 3 samples then you will produce 3 bam files. I use BWA / Samtools for this.
4. Take your co-assembled contigs and bam files and load them into GroopM using 'groopm parse' saveName contigs.fa bam1.bam bam2.bam...
5. Keep following the GroopM workflow. See: groopm -h for more info.

Licence and referencing

Project home page, info on the source tree, documentation, issues and how to contribute, see

If you use this software then we'd love you to cite us.
Our paper is now available as a preprint at The DOI is

Copyright © 2012-2014 Michael Imelfort.

GroopM is licensed under the GNU GPL v3
See LICENSE.txt for further details.

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